Metatranscriptomic Analysis of Lactic Acid Bacterial Gene Expressions during Kimchi Fermentation

Kimchi is a traditional Korean food that is fermented from various vegetables. Here, a metatranscriptomic approach was applied to assess comprehensively gene expressions of kimchi microbiome during the kimchi fermentation. Metatranscriptomic mRNA from periodic five kimchi samples was extracted and sequenced by Illumina GA IIx. Community analyses revealed that the kimchi fermentation was governed predominantly by three LAB genera Leuconostoc, Lactobacillus, and Weissella. The metabolic assignments of mRNA sequencing reads using MG-RAST also revealed a genetic characteristic of lactic acid bacteria (LAB); carbohydrate metabolisms and lactic acid fermentation were key categories. Therefore, the mRNA sequencing reads were mapped to the genomes of three LAB strains, J18, 23K, and KACC 15510, which were representative strains of Leuconostoc, Lactobacillus, and Weissella, respectively. The mapping analysis showed that Leuconostoc was active during the early stage, whereas expressions of Lactobacillus and Weissella were high at the middle or late stages. However, gene expressions of Lactobacillus were rapidly dropped at 25 days, which might be caused by bacteriophage infections of Lactobacillus species. Mannitol was produced by only Leuconostoc containing two copies of mannitol dehydrogenase (MD) genes coded on the chromosome and plasmid, respectively. Interestingly, the chromosomal MD gene was active at the early stage, whereas the other plasmid MD gene expressed actively at the late stage. In addition, expressional analyses of genes related to carbohydrate transports, pH tolerance, and carbohydrate hydrolysis were also investigated. Overall, these results provide indigenous gene- and taxon-specific expressional information during the kimchi fermentation and also expand our understandings of fermentation processes by complex microbial communities.